Congrats! Hope you enjoy your sweet new ride!
#1 1994 and 2000 both have 8.8 inch rear ends. The differential parts will probably swap out but i'm making no promises otherwise. The track width could be different. FLM could have changed the control arm design and mounting locations between years, who knows.
You are correct about the internals but the housing will not interchange. 91-97 interchange, 98-02 interchange and have the Watts Linkage, and 03+ interchange and have different mounting and width for the new FWD offset wheels.
#2 I think the PI heads went into the TC in 2003. I read in a thread somewhere in this forum that 2003 may have been the only year they were used, which would explain why the 2008 only makes 235 HP when the 2003 made 245ish. Interestingly enough, the 2003 TC was classified as a ULEV vehicle (hilarious, really).
Wrong, 01 was the first year for PI engines in all Panthers (PI is more than just heads) 2003 was the first year for the new frame, 05 got throttle by wire.
#3 Look under the dash to the right of the steering column.
#4 I'd be surprised if they are, 6 years is a long time, especially when two design variations of the vehicle have been made over that period.
The Window motors are different, the 98 redesign completely changed the door design.
As far as the brakes go, thats a good question. Compare the parts to one another. You may be surprised. I believe the 2000 TC is heavier than the '94, which would require you to have more breaking power available.
I did have a neighbor who a couple years ago put new rotors on a '95. The fronts were different from the '91-94 cars only in that some kind of anti-corrosive coating was on the non-friction surfaces of the '95 rotor. He chose to use the older model part instead and had no problem. I suggest you compare the parts first. If there is ANY dimensional difference (thickness, diameter, other dimentions in relation to the hub) don't use the old parts. If changes were made to the part to improve heat dissipation or increase maximum braking force then you could be creating a safety hazard by using the old brakes.
91-97 Town Cars all had the same brakes. In 98 all the Panthers got upgraded front brakes requiring 16" wheels or larger in the front. 03+ brakes are different due to the new wheel offset and suspension redesign. The rear brakes have stayed very similar through the years.
Enjoy your ride!